Dynamics of DNA molecules in a cross-slot microchannel

Abstract

The conformation and dynamics of double-stranded DNA molecules in cross-slots with equal arm length are examined with the use of fluorescent labeled λ-DNA at 1.2 ⩽ De ⩽ 4.1. The stretching and diffusing of individual DNA molecules in the flow was visualized/recorded with confocal laser scanning microscopy (CLSM). The onset of coil–stretch transition of DNA molecules in the elongational flow was determined at the microscale. Time-dependent velocity distribution with a mean velocity of 50 µm s−1 for DNA molecules was observed by using FluoSpheres, carboylate-modified microspheres over a time period of 1.12 s. The effect of channel geometry (corner and outlet regions) and the solution viscosity (1.9 cP and 9.5 cP) on the conformation and diffusion are also studied and discussed. We report the maximum and the distribution of the fractional extension of DNA molecules, and show that the maximum fractional extension may be up to 0.64 at De = 4.1, and at a strain of 1.8 there is a corresponding stretching force of about 200 pN.

DNA molecule stretching through thermo-electrophoresis and thermal convection in a heated converging-diverging microchannel

“…As expected, the temperature effect had a significant influence on extension. Unlike those in Hsieh et al [2] or Hsieh and Liou [3], the present stretching behavior at a temperature of 55°C changed following the evolution of double strand, transition, and single strand, based on CLSM in situ observation. Even so, similar linear dependence behavior was still found with different slopes.…”

“…Both approaches have their own advantages/disadvantages which depend on the particular application. For the former, with fluorescently labeled DNA molecules, it is possible to visualize the change in the conformation of a single DNA molecule under an optical microscope [2,3]. …”

DNA molecule dynamics in converging–diverging microchannels

“…The CLSM measurement set‐up and its working principle (as shown in Figures 4a and 4b respectively) followed that described by Hsieh et al [9], with a slight modification for the flow cell and the flow circulation loop. For that reason we shall not repeat all the details here.…”

“…The present study is a continuation of our previous endeavours [9] to examine the dynamics and conformation of DNA molecules in a pressure‐driven flow through a converging–diverging square microchannel using both CLSM (confocal laser scanning microscopy) and MPIV (microparticle image velocimetry) measuring/visualization techniques. Figures 1 and 2 show schematically the gradual (Figure 1) and sudden (Figure 2) flow‐cell systems used in the present study.…”

Numerical simulation of viscoelastic fluids in cross-slot devices

“…Findings revealed that the bifurcation was unaffected by the rounding of the corner, but rather controlled by the extensional properties of the constitutive model, with a reduction in the level of the critical We for bifurcation as extensibility increased. More recent research has focused on microfabricated cross-slot devices, specifically in accurate and low cost methods for studying DNA [20].…”